Where's Molly?
by meggykate
Summary: Molly and her son go missing. Mycroft and Sherlock must find them before it's too late. Mollcroft
1. Chapter 1

Prologue

Sherlock Holmes burst through the St. Bart's Morgue "She's not in her office" he said to his best friend Dr. john Watson. "That's not like her Lestrade said he called and told we were coming" said John. Sherlock noticed the intern in the corner cleaning tools. "Where's Dr. Hooper?" the woman jumped, and turned around "She uh went out on her 15 minute break over an hour ago I just assumed she was helping you in the lab." Sherlock turned in a panic and ran out of the morgue. "Thanks Michelle" John shouted over his shoulder as he ran after Sherlock.

"Sherlock? hey what's going on?" John asked as he finally caught up to the lanky detective. "Call Lestrade tell him to collect Mary and go to Baker St." "What's going on Sherlock?" They walked into the hospital childcare center and were immediately stopped by the woman in charge. "Oh Thank God Mr. Holmes we were about to call your brother." John's heart sank "About an hour ago Kate took Finn to change his pull up and we can't find either of them now." "Where's his cot?" Sherlock asked. The first thing they noticed was the blue and white striped blanket laying on the floor besides the child's assigned cot. At 2yrs old Finn took that blanket everywhere he went. Picking up the blanket Sherlock saw a note on the floor, "Sherlock what does it say?" John asked, trying to read the piece of paper

"Dearest Mycroft,

Thanks for taking care of my family but, I think I'll be taking them back now.

-M"

Sherlock got on his phone right away. "Mycroft you've been compromised."

A black car was waiting for then outside the hospital. "Brother Mine how did you let this happen?" asked Sherlock as they climbed in. "Her security team are all dead, Kate the agent I put in place was turned at some point." John shivered he'd never seen Mycroft this angry before and he almost pitied whoever took Molly and their son. "Who took them, and why are they claiming that Molly and Finn, are their family?" he asked, pulling the brothers from their silent conversation. "It's Moriarty, and I'll explain when we reach my house." Mycroft said. "Is that wise dear brother you've been compromised." "You know it is!" shouted Mycroft leaving everyone in a stunned silence. "What about Mary and Lestrade? John asked a few minutes later worried about the safety of his fiancee now knowing Moriarty's back. "I texted them already, they're on their way was we speak." Mycroft said before getting back on his phone.

To call Mycroft and Molly's home a house would be a great understatement, and Estate or even a Compound would be more like it. Anthea, Mycroft's PA, came out of the house to greet them. "Sir they found Agent Hunter she's barely alive we're bringing her to The Base." "Thank you let me know when she's awake, make sure their are guards outside the door." John had only been in their house a few times while the home's classic-ness reeked of Mycroft, he could see Molly in the touches of bright colors around the house. John immediately rushed to Mary's side when they entered the study "What's going on?" she whispered, "Lestrade just grabbed me from work, and now we're sitting in some study with a woman who only talks to Lestrade." John chuckled, "This is Molly and Mycroft's home, and that woman is Anthea Mycroft assistant, she only talks to Lestrade because there might be something going on between the two no one knows for sure since one rarely speaks, and the other won't say a word about it." "Mycroft what's going on? why are we here and not out looking for Molly and Finn?" Lestrade asked. "First, Whatever I am about to say stays in this room between this group understood?" Mycroft asked as he took his suit jacket off. After getting everyone to agree he took a seat behind his desk. "Good, please do not judge Molly until you have to whole story. Finn is not my son." Everyone turned and looked dead at Mycroft, "What?!" gasped Lestrade. "Finn is Moriarty's son." 


	2. Chapter 2

AN: Hopefully this fixes the problem thank you Monirosez for pointing out there was a problem!

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>Why would Molly even do something like that? John asked, after the initial shock had started to wear off. She was all goo goo eyed for Sherlock at the time added Lestrade. How do you think Moriarty celebrated bombing an elderly home? Mycroft asked. He thought he could get on over on me prove he wasn t gay, at least to Molly, and keep her in his back pocket said Sherlock. Kind of like you toying with her emotions? Mary asked. How many times am I going to apologize for that? I don t do that anymore. Yeah probably because your brother would have your head. As much as Sherlock denied it even he knew not to cross the British Government when it came to his wife. So then how did you get involved? Because this is all too weird for me to figure out. asked John as he put his tea cup on the side table.<p>

Molly walked out of her Doctors office stunned, This wasn t suppose to happen to me she thought. Before she could take a step off of the curb, a black sleek car pulled up. Door swung open Miss Hooper get in. said a beautiful woman in business attire. No thanks, I don t get into strange cars. Molly replied briskly. Miss Hooper my boss is not a patient man, get in the car. Molly s phone began to buzz, pulling it out of her pocket she read the message That is my PA, please get into the car.-MH.  
>Molly sighed, didn t Mycroft Holmes have better things to do than harass her some more. After the whole Great Game as John had called it on his blog, Mycroft had Molly picked up by his men and taken to some secret building and interrogated her there for hours. Fine you win Mycroft she said out loud, and climbed into the car, where the PA kept her her attention on her phone.<br>This time instead of an interrogation room Molly was escorted into an office, while she waited she let her mind wander trying to imagine what her life would be like if she decided to go through with this.

Miss Hooper apologies for keeping you waiting. Mycroft said startling Molly from her thoughts. It s Doctor and you know. It what do you want Mycroft. To say Molly despised the man sitting behind the desk would be an understatement. Doctor Hooper what are your plans? Plans for what exactly Mycroft? What are you going to do about your pregnancy? Molly opened and closed her mouth a few times before she started to cry. You know when I thought about finding out I was pregnant it s be a happy, joyous moment. I d be married and husband would be there just as excited as I was. Never in my mind did I think I d end up pregnant by a psychopath who tried to kill my friends. God must have wanted a real good laugh when he made me. And no I don t know what my plans are. Mycroft sat back in his chair, people crying always made him uncomfortable, well any display of emotion made him uncomfortable. While his rise to the top of the British Government had earned him the nickname The Ice Man he did feel pity for the young pathologist. Doctor Hooper you understand my need to see how this situation will be handled this isn t some random person off the street this is a madman who is hell bent on killing my brother and trying to take down this government. Just call me Molly, and yes I get that, but it s not an easy decision. I ve always wanted to be a Mum just not like this. I think you made your decision already Molly he said coolly. He couldn t believe she was going to actually go through with this, to have that man s child. He watched as Molly s face turned red with anger, she stood up and collected her things. Turning to face him pointing her finger right at him Mycroft Holmes you know as well as I do that children often turn out to be the opposite of their parents, just look at your family. With that she stormed out of his office. Anthea walked in, Keep surveillance on her, I want to know if he tries to contact her. he said without even looking up from his desk.

It would be 5 months, 2 after Sherlock s fall that the letters and gifts began showing up to Molly s flat. At first they were a little weird, Molly thought it was a kid just messing around. It wasn t until Moriarty s 2nd in command showed up at her flat. At 7 months Molly was down to part time and desk duty at the morgue, or at least that s what HR said. Molly knew it was because of all the false Sherlock is a fraud stories and how she used to help him in the lab. She thought back to the 2 nights he spent in her flat after the fall, his apology for not watching out for her more, he felt guilty that she was in this situation because of him. This was the most he had opened up to her since they were in Uni. he must have been feeling very vulnerable after the fall she thought. Molly opened the door to her flat, throwing her bag and keys on the side table, she slipped her shoes off, all she wanted to do was take a nice long hot bath and climb into bed, the stress of everything weighing her down. Good of you to finally come home Molly. man s voice broke through her thoughts. Molly startled tried to run but was grabbed and thrown on her love seat. I have a message for you Miss Hooper he growled as she tried to fight him off. Please just take whatever leave me and my child alone. I won t say a word. she cried Please. she begged. Sebastian Moran laughed loosening his hold on her. Miss Hooper boss is not happy that you chose to help his enemy. The only thing keeping you alive right now is that your are carrying the heir to the Moriarty Empire. He pulled a knife out.  
>Sir, all surveillance in Miss Hooper s flat and the building itself are down. said Anthea.<br>Mycroft got up Get me my car now! he shouted. 


	3. Chapter 3

_AN: OK so Mycroft's OOC but I think he'd give Molly a chance seeing as how she saved his brother's life. For some reason everytime I upload my chapters my punctuation keeps disappearing so thanks Anon reader for for pointing that out once again. If it bothers anyone this is also posted on Ao3. Hopefully this works I had to sneak trying to fix this at work._

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><p>The door to Molly s flat was ajar. Mycroft quietly pushed it open and entered the flat after making sure no one else was in the flat Mycroft and Anthea turned their attention to Molly. Before either could say a word Dr. John Watson limped into the flat rushing over to Molly s side.<br>"John what are you doing here?" Mycroft asked. John with gun in this hand turned to Mycroft "Molly called me, it might have been accidental cuz all I heard was a struggle and the mumbling of a man s voice." John said looking down at a bruised and battered Molly. "Thank you for coming John can you please look Molly over?" "Molly where's your first aid kit?" John asked looking her over more closely. "I-It s in the kitchen." Molly finally replied.

After John left the room Molly painfully turned to Mycroft and Anthea "What are you doing here?" she hissed. Anthea turned and knelt down next to Molly who sat up on the loveseat. "We've been monitoring you to make sure none of Moriarty's men caught wind of you helping Sherlock." said Anthea. "So you've been having me followed are their camera's in here?" Molly asked as she suddenly looked around the flat. "No team, and no cameras in your flat just ones in the hall and outside your building, It's only been Anthea and I, who have been watching you, I can't let on that I know my brother's alive, John's coming back we'll talk afterwards." Mycroft said his voice a touch softer.

Molly was so confused first, Mycroft was dragging her into his office telling her to get rid of her child and threatening her to running to her flat after she got attacked. John began attending to her "Molly what happened?" he asked. "I-I ca-came home and Sebastian Moran was hiding in my flat I had met him when I was with Jim." She noticed John flinch when she said Jim's name. Mycroft gave her a look to not let on to John about Sherlock. "I don't know if he was mad because Jim's dead, and took it out on me for having known Sherlock." "Why wouldn't he come after me?" John asked "Maybe because he figured Molly couldn't protect herself in her state" supplied Anthea. "Speaking of that, we really need to get you to a hospital to get the baby checked out." "I've called a Doctor in my employ. Molly are you alright to walk down to the car?" Mycroft asked as he helped her stand. "Why are you here Mycroft?" John blurted out, it's been no secret since Sherlock s death that whatever civility John had for Mycroft was gone. Before Mycroft could reply Anthea spoke "Because Dr. Watson, Mr. Holmes has a personal stake in this." she nodded towards Molly's 7 months protruding belly. Molly looked at her stunned, what was Miss Anthea's Not My Real Name playing at? Everyone knew Sherlock wouldn't touch her if she was the last woman on earth. "You're carrying.." "No not Sherlock's. John was so stunned he didn't notice the glances between the other three in the room.

Since John had insisted on accompanying them sitting in the exam room was the only time Mycroft and Molly could be alone since. "Mycroft why did Anthea say that?" Molly asked. Mycroft could hear the anger and confusion in her voice. "Anthea's right if people think it's mine I can protect you better. I can get a team and it won't arouse suspicion about my brother." "No Mycroft you have given me hell and you think I m just going agree to this?" Molly yelled. "Molly a man broke into your flat and carved JM into your hip luckily John's too depressed and he missed that. Who's to say that he won't come back? What if he kills you?" " Why do you care? You were ready to throw me into some top secret jail cell, and now all of a sudden all this?" Mycroft walked over to her taking her hand. "Molly, Sherlock trusted you with his life. You know that his trust is something he doesn't give away freely. I apologize for the way I treated you." Before Molly could even reply the Doctor came in greeted Mycroft and gave her a sympathetic smile. She never learned the Doctor's name but he was kind, as he stitched up the Moriarty's initials carved into her. The baby was fine and very active during her scan, and Molly could relax a bit with that good news.

Mycroft had Anthea escort Molly back to his estate. "Am I going to be locked up in his home for the rest of my life?" Molly was wandering around the study looking upon the books. Anthea looking up from her phone watched her for a minute "Molly this has been an awful day for you. I know you and Mycroft aren't seeing eye to eye on any of this but he does care about your safety. He'll never show it but he realizes he misjudged you." Molly snorted "He made a mistake with you just like Moriarty did in underestimating you and I think that bothers him." Molly sat in the chair by the fireplace absently running her hand over her big belly thinking back to how she ended up here, how she must have done something to piss someone off somewhere in a past life. This was suppose to be a happy time, a time she would share with her husband starting a family. No not shy, weird Molly Hooper, all the kids from primary school who made her life a living hell, would be laughing at her if they knew how her life turned out. Pregnant by a psychopath, now in hiding because of said psychopath who haunted her even in his death. Molly jumped out of her chair and ran as fast as her large body would let her. "Molly what's wrong here sit." Anthea pulled out a chair and waited for the woman to catch her breath "Moran, Moran he said that Jim was alive. Th-th-that they know Sherlock's alive. Jim can't be alive. I did his post mortem, there was brains everywhere. Could he have said that to scare me? Why didn't I think of this until now? Is Sherlock in danger?" "Molly it's alright you need to calm down this has been too much excitement for the baby. I need to get back to the office, would you feel better if Dr. Watson was here with you until Mycroft or myself return?" Molly nodded her head yes.

Molly and John didn't see Mycroft until the next evening, John quietly made his leave, but not before threatening Mycroft if he hurts Molly whatsoever. "You brought Toby!" Molly exclaimed as she picked the evil ball of fur. That cat had Mycroft chasing him through Molly s flat for over an hour. "I brought some comforts from your flat, I apologize for making you come here but you're in danger and until we know more you have to stay put. If you could come into the study with me we have some things to discuss." Once Molly and Mycroft were settled into the chairs by the fireplace Mycroft began "One of Sherlock's homeless network was part of Moriarty's network and he assisted with Sherlock's fake death. As far as I can tell, they think Sherlock's just in hiding, that's why Moran came after you hoping you'd get Sherlock out of hiding. It's why you've been receiving those threatening letters. Why didn't you tell me about them or if you didn't want to why didn't you go to DI Lestrade?" "I just thought it was some kids joking around until yesterday. I didn't even know Jim knew I was pregnant, he must have been keeping tabs on me." "Sherlock and I think it would be in your best interest to continue this farce of a relationship Anthea thought up. If we were to marry I could get a security team I can have you and of course your child protected. Not arousing suspicion from my colleagues. You do need to sign a Secrets Act and I can forge the marriage certificate without us actually having to go to a Registrar's office." "Is Anthea ok with all of this I know she only said we were together as a cover?" She could feel the blush spread across her cheeks, if Mycroft noticed he made no mention of it. "Why would my PA care if we were quote unquote married?" Her face was getting even hotter "W-well ar-aren't you two uh you know?" Mycroft laughed pulling Molly into an even further embarrassment "Adrianne is married to a field agent, I do not have time for such _romantic entanglements_ Dr. Hooper." "Apologies _Mr. Holmes_ I just thought since I've never seen you two apart." "We're getting off track, Uh yes we are I'll let you think on our arrangement, but I need an answer by tomorrow morning the latest." Mycroft got up and made towards the door, "Mycroft can you really keep my child safe, I never asked for any of this I swear, and if Jim is really alive I need to know that my son will be ok. I know his Dad is who he is but I don't believe my son will be like his father if I can help it. I need to know if you can keep us safe I don't want Jim to even lay an eye on him. I'm so scared he's going to hurt him not even me, but my child and I can't" the tears were falling hard. When she looked up Mycroft handed her his handkerchief, she saw something flash across his face. "Molly I promise I will do everything in my power to make sure you both are safe." The silence passed for what felt like for hours until he heard her whisper "Yes ." They stayed up late into the night coming up with their cover story making sure they were on the same page. Molly finally went to bed curling up with Toby feeling relieved as sense of calm washed over her she hadn't felt like this since before a psychopath came into her life.


End file.
